Mercurial > repos > kkonganti > cfsan_cronology

comparison cfsan_cronology.xml @ 10:ddf7a172bf30

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"planemo upload"
author kkonganti
date Wed, 29 Nov 2023 10:53:42 -0500
parents a3c1cba6f773
children a5f31c44f8c9
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9:5eaaf749472c 10:ddf7a172bf30
81 help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/> 81 help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)."/>
82 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" /> 82 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
83 </inputs> 83 </inputs>
84 <outputs> 84 <outputs>
85 <data name="multiqc_report" format="html" label="cronology: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/> 85 <data name="multiqc_report" format="html" label="cronology: MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
86 <data name="mashtree" format="nwk" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/> 86 <data name="mashtree" format="newick" label="cronology: Genome distance based tree on ${on_string}" from_work_dir="hitsTree.dnd"/>
87 <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}"> 87 <collection name="itol_metadata" type="list" label="cronology: iTOL Metadata: ${on_string}">
88 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" directory="./cpipes-output/cat_unique" match_relative_path="true" /> 88 <discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" ext="txt" directory="./cpipes-output/cat_unique" match_relative_path="true" />
89 </collection> 89 </collection>
90 <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}"> 90 <collection name="gene_models" type="list" label="cronology: Predicted gene models: ${on_string}">
91 <discover_datasets pattern="(?P&lt;name&gt;.*)\.gff" ext="gff" directory="./cpipes-output/prokka" recurse="true" match_relative_path="true" /> 91 <discover_datasets pattern=".*\/(?P&lt;name&gt;.*)\.gff" ext="gff" directory="./cpipes-output/prokka" recurse="true" match_relative_path="true" />
92 </collection> 92 </collection>
93 <collection name="assemblies" type="list" label="cronology: Polished genome assemblies: ${on_string}"> 93 <collection name="assemblies" type="list" label="cronology: Polished genome assemblies: ${on_string}">
94 <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fa" directory="./cpipes-output/polypolish" match_relative_path="true" /> 94 <discover_datasets pattern="(?P&lt;name&gt;.*)\.fa" ext="fa" directory="./cpipes-output/polypolish" match_relative_path="true" />
95 </collection> 95 </collection>
96 </outputs> 96 </outputs>